Research workbench
Crystal structure of laccases from pycnoporus sanguineus, izoform I
Analyse Crystal structure of laccases from pycnoporus sanguineus, izoform I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NQ7
- Type
- protein
- Length
- 497 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laccase
- EC
- 1.10.3.2
- UniProt
- D7F485
- Ligands
- NAG, BMA, MAN, CU, PER
- Pockets
- 5 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Laccase (EC 1.10.3.2) | protein | 497 | 12% helix, 38% strand | D7F485 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A
- CU · Copper (II) ion · metal · 4 copies · chains A
- PER · Peroxide ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.50 | 0.80 | 19 | empty |
| 2 | 199 | 0.49 | 0.76 | 32 | empty |
| 3 | 83 | 0.41 | 0.79 | 20 | empty |
| 4 | 103 | 0.36 | 0.74 | 13 | empty |
| 5 | 53 | 0.34 | 0.78 | 17 | empty |
Modifications
Observed in the structure: 3 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 5NQ7 · Crystal structure of laccases from Pycnoporus sanguineus, izoform I · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt D7F485
- Elsewhere: RCSB PDB 5NQ7 · PDBe 5NQ7 · UniProt D7F485
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